Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	657,676	0	A	C	51.2%	43.8 / 66.9	43	V88G (GTG→GGG)	flc	fluoride efflux channel, dual topology membrane protein
Reads supporting (aligned to +/- strand):  ref base A (16/5);  new base C (0/22);  total (16/27)
Fisher's exact test for biased strand distribution p-value = 7.67e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.10e-07

GGTCTTTAGTGTGCGGTTGAGGCCGAAAACAGCCAGAATGCCAGTGCGGTCATGGCAAAAGACCCC‑AGAAGGTTGACGAAAACGTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCGAATCCTATTCCTATGATGAATGCCCCAATCAGG  >  NC_000913/657550‑657816                                                                                                                                 |                                                                                                                                             ggTCTTTAGTGTGCGGTTGAGGCCGAAAACAGCCAGAATGCCAGTGCGGTCATGGCAAAAGACCCC‑AGAAGGTTGACGAAAACGTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTgaga                                                                                                                      >  1:725486/1‑151 (MQ=255)   tCTTTAGTGTGCGGTTGAGGCCGAAAACAGCCAGAATGCCAGTGCGGTCATGGCAAAAGACCCC‑AGAAGGTTGACGAAAACGTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAg                                                                                                                    <  2:368420/151‑1 (MQ=255)         gtgtGCGGTTGAGGCCGAAAACAGCCAGAATGCCAGTGCGGTCATGGCAAAAGACCCC‑AGAAGGTTGACGAAAACGTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAGgttgtt                                                                                                              >  2:129125/1‑151 (MQ=255)                          aaaaCAGCAAGAATGCCAGTGGGGTCATGGCAAAAGACCCC‑AGAAGGTTGCCAAAAACTTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACCCCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATc                                                                                              <  2:406221/150‑1 (MQ=255)                                 ccAGAATGCCAGTGCGGTCATGGCAAAAGACCCC‑AGAAGGTTGACAAAAACGTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACCCCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCggt                                                                                          <  2:469350/147‑1 (MQ=255)                                    gAATGCCAGTGCGGTCATGGCAAAAGACCCC‑AGAAGGTTGACGAAAACGTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGAtt                                                                                   >  2:372673/1‑151 (MQ=255)                                    gAATGCCAGTGCGGTCATGGCAAAAGACCCC‑AGAAGGTTGACGAAAACGTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGAtt                                                                                   >  1:466879/1‑151 (MQ=255)                                     aaTGCCAGTGCGGTAATGGAAAAAGCCCCA‑AGAAGGTTGACAAAAACGTCCATTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACCCCACTTCTGCCGAAAATTTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGAtt                                                                                   <  2:709578/150‑1 (MQ=255)                                       tGCCAGTGCGGTCAGGGCAAAAGCCCCC‑AGAAGTTTAACAAAACCTTTCAGTAATGCCCAGCAAAA‑GCGGCCCTCTTGTAAAAAAAACCCCCCTTCTGCCGAAAATTTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAAt                                                                                <  2:83293/151‑1 (MQ=255)                                         ccggggCGGTCAGGGAAAAAGCCCCC‑AGAAGGTTGACAAAAACGTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACCCCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATAc                                                                              <  2:216241/146‑1 (MQ=255)                                         ccAGTGCGTTCATGCAAAAAGCCCCC‑AGAAGGTGGACGAAAACGTTCAGTAATCCCCGGCAAAA‑GCGGCCCTTTTTTAACAAAAACCCCACTCCTCCCAAAAATGTTAAAAAGGTTTTTAGACCGCCACAAAATCCGGTGGTGATTAATAc                                                                              <  2:301954/151‑1 (MQ=255)                                         ccAGTGCGGTCAGGGCAAAAGCCCCC‑AGAAGGTTGACGAAAACGTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACCCCCCTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATAc                                                                              <  2:809879/151‑1 (MQ=255)                                         ccAGTGCGGTCAGGGAAAAAGACCCC‑AGAAGGTTGACGAAAACGTTCAGTAATGCCCAGCAAAA‑GCGGCCCTCTTGTAACAAAACCCCCACTTCTGCCGAAAATGTTGGGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATAc                                                                              <  2:770574/151‑1 (MQ=255)                                            gTGCGGTCATGGCAAAAGACCCC‑AGAAGGTTGACGAAAACGTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACttt                                                                           >  2:616280/1‑151 (MQ=255)                                            gTGCGGTCATGGCAAAAGACCCC‑AGAAGGTTGACGAAAACGTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACttt                                                                           >  2:192884/1‑151 (MQ=255)                                                 gTCATGGCAAAAGACCCC‑AGAAGGTTGACGAAAACGTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCcaca                                                                      >  2:766612/1‑151 (MQ=255)                                                    cagggaaaaaaCCCCAAGAAGGTAGACAAAAACGTACAGAAGGCCCCACACAAA‑GCGGCCTTATTAAAAAAAAAACCCCACTTCTGCAGAAAATGTTGAAAGGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCacac                                                                     <  1:410729/145‑1 (MQ=255)                                                       gCAAAAGACCCC‑AGAAGGTTGACGAAAACGTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGAt                                                                >  1:173625/1‑151 (MQ=255)                                                          aaaGCCCCC‑AGAAGGTTGACAAAAACGTTAATTAACGCCAAGCCAAA‑GCGGCCCTTTTGTAACAAAAACACCCCTTCTGCCAAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCaa                                                             <  2:492201/151‑1 (MQ=255)                                                          aaaGACCCC‑AGAAGGTTGACAAAAACGTTCAGTAATCCCCAGCAAAA‑GCGGCCCTCTTGTAAAAAAAACCCCACTTCGGCCAAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCaa                                                             <  2:595380/151‑1 (MQ=255)                                                              ccccc‑AGAAGGTTGACAAAAACGTTCATTAATGCCCAGCCAAG‑GCGGCCCTCTTGAAACAAAAACCCCCCTTCTGCCGAAAATGTTGAGAAGGTTTTAAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATg                                                           <  2:264692/148‑1 (MQ=255)                                                              aCCCC‑AGAAGGTTGACGAAAACGTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAAAAAAAACCCCCCTTCTGCCGAAAATGTTGAGAAGGTTTTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATg                                                           <  2:221285/149‑1 (MQ=255)                                                                            gACGAAAACGTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCctg                                               >  2:290861/1‑148 (MQ=255)                                                                               aaaaaCTTTCAGTAATGCCCAGCCAAG‑GCGGCCCTTTGTTAAAAAAAACCCCACTCCTGCCGAAAATGTTGAGAGGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAAc                                         <  1:421508/150‑1 (MQ=255)                                                                                aaaaCTTTCAGTAATGCCCAGCCAAA‑GCGGCCCTTTTTAAAAAAAAACCCCACTGCTGCCAAAAATGTTGAGAAGGTTTTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAAc                                         <  2:716750/150‑1 (MQ=255)                                                                                     gTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCg                                   >  2:467575/1‑151 (MQ=255)                                                                                     gTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCg                                   >  2:393452/1‑151 (MQ=255)                                                                                     gTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCg                                   >  2:439992/1‑151 (MQ=255)                                                                                      ttCAGTAATGCCCAGCCAAG‑GCGGCCCTTTTGTAACAAAAACCCCACTTCTGCAGAAAATTTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCg                                   <  2:474333/150‑1 (MQ=255)                                                                                        cAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCGAAt                                >  2:332434/1‑151 (MQ=255)                                                                                           tAATGCCCAGCAAAG‑GGGGCCTTCTGGTAACAAAAACACCACTTCTGCGGAAATTGTTGAAAAGGTTGTGAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCGAAtcc                              <  1:44264/150‑1 (MQ=255)                                                                                                ccgaGCAAAG‑GCGGCCCTCTTGTAACAAAAACCCCCCTGCGGCCAAAAATGTTGAGAGGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCGAAtcctattcc                        <  1:449670/148‑1 (MQ=255)                                                                                                cccGGCGAAA‑GCGGCCCTCTTGAAAAAAAACCCCCCCTTCTGGCAAAAATGTTGAGAAGGTTGTTAGTCCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCGAAtcctattcc                        <  2:119134/151‑1 (MQ=255)                                                                                                ccaaGCCAAG‑GGGCCCCTTTTGTAACAAAAACACCACTGCTGCCAAAAATGTTGAAAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCGAAtcctattcc                        <  1:475685/148‑1 (MQ=255)                                                                                                   caccAAAGGCGGCCTTCTTGAAAAAAAAACCCCACTCCTGCCAAAAATGTTGAGAAGTTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCGAAtcctattccta                      <  1:101632/149‑1 (MQ=255)                                                                                                   aGCCAAA‑GCGGCCCTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCGAAtcctattcctat                     >  1:77643/1‑151 (MQ=255)                                                                                                      caaaggCGGCCTTTTTATAACAAAACCCCCCCTTCTGCGGAAAATGTTGAGAAGGTTTTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCGAAtcctattccta                      <  1:128087/143‑1 (MQ=255)                                                                                                       aaa‑GCGGCCCTCTTGAAACAAAAACCCCCCTTCTGCCAAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCGAATCCTATTCCTatgatg                 <  2:339086/151‑1 (MQ=255)                                                                                                       aaa‑GCGCCCCTTTTGTAACAAAAACCCCACTTCTGCCAAAAATGTTGAGAAGTTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCGAATCCTATTCCTatgatg                 <  1:789728/151‑1 (MQ=255)                                                                                                        aagggggCCTTCTAGAAAAAAAAACCCCACTTCTGCCGAAAAGGTAGAGAGGTTTTTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCGAATCCTATTCCTatgatg                 <  2:655454/146‑1 (MQ=255)                                                                                                               cccTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTCGATCAATGTTCGTCATTCTGCTGAACCATGCGAATCCTATTCCTATGATGAATGcc           >  1:172942/1‑150 (MQ=255)                                                                                                                      gTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCGAATCCTATTCCTATGATGAATGCCCCAATCAg   >  1:226152/1‑151 (MQ=255)                                                                                                                       aaaCAAAAACACCACTTCGGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCGAATCCTATTCCTATGATGAATGCCCCAATCAgg  <  1:21280/150‑1 (MQ=255)                                                                                                                                 |                                                                                                                                             GGTCTTTAGTGTGCGGTTGAGGCCGAAAACAGCCAGAATGCCAGTGCGGTCATGGCAAAAGACCCC‑AGAAGGTTGACGAAAACGTTCAGTAATGCCCAGCCAAA‑GCGGCCCTCTTGTAACAAAAACACCACTTCTGCCGAAAATGTTGAGAAGGTTGTTAGACCGCCACAAAATCCGGTGGTGATTAATACTTTCCACACTGGATCAATGTTCGTCATCCTGCTGAACCATGCGAATCCTATTCCTATGATGAATGCCCCAATCAGG  >  NC_000913/657550‑657816

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑